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Cardoso AL, Venturelli NB, da Cruz I, de Sá Patroni FM, de Moraes D, de Oliveira RA, Benavente R, Martins C. Meiotic behavior, transmission and active genes of B chromosomes in the cichlid Astatotilapia latifasciata: new clues about nature, evolution and maintenance of accessory elements. Mol Genet Genomics 2022; 297:1151-1167. [PMID: 35704117 DOI: 10.1007/s00438-022-01911-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
Abstract
Supernumerary B chromosomes (Bs) are dispensable genetic elements widespread in eukaryotes and are poorly understood mainly in relation to mechanisms of maintenance and transmission. The cichlid Astatotilapia latifasciata can harbor Bs in a range of 0 (named B -) and 1-2 (named B +). The B in A. latifasciata is rich in several classes of repetitive DNA sequences, contains protein coding genes, and affects hosts in diverse ways, including sex-biased effects. To advance in the knowledge about the mechanisms of maintenance and transmission of B chromosomes in A. latifasciata, here, we studied the meiotic behavior in males and transmission rates of A. latifasciata B chromosome. We also analyzed structurally and functionally the predicted B chromosome copies of the cell cycle genes separin-like, tubb1-like and kif11-like. We identified in the meiotic structure relative to the B chromosome the presence of proteins associated with Synaptonemal Complex organization (SMC3, SYCP1 and SYCP3) and found that the B performs self-pairing. These data suggest that isochromosome formation was a step during B chromosome evolution and this element is in a stage of diversification of the two arms keeping the self-pairing behavior to protect the A chromosome complement of negative effects of recombination. Moreover, we observed no occurrence of B-drive and confirmed the presence of cell cycle genes copies in the B chromosome and their transcription in encephalon, muscle and gonads, which can indicates beneficial effects to hosts and contribute to B maintenance.
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Affiliation(s)
- Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Natália Bortholazzi Venturelli
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Irene da Cruz
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Fábio Malta de Sá Patroni
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Rogério Antonio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, Brazil
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil.
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Polygenic sex determination produces modular sex polymorphism in an African cichlid fish. Proc Natl Acad Sci U S A 2022; 119:e2118574119. [PMID: 35357968 PMCID: PMC9168840 DOI: 10.1073/pnas.2118574119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceSex differences in traits can occur when those traits are modified by genetic factors inherited on sex chromosomes. We investigated how sex differences emerge in a species with more than one set of sex chromosomes, measuring a variety of morphological, physiological, and behavioral traits. Rather than exhibiting sexual dimorphism associated with primary sex, the species has higher-order sexual polymorphism in secondary sexual characteristics or more than two phenotypic sexes. Variation in secondary sexual characteristics is modular, involving the interplay of sex-linked and sex-limited traits. Our findings provide implications for how sex determination systems and whole-organism fitness traits coevolve, including that significant creation or loss of variation in diverse traits can occur during transitions among sex chromosome systems.
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3
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B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription. Life (Basel) 2021; 12:life12010050. [PMID: 35054443 PMCID: PMC8781039 DOI: 10.3390/life12010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/17/2022] Open
Abstract
B chromosomes (Bs) are highly polymorphic additional chromosomes in the genomes of many species. Due to the dispensability of Bs and the lack of noticeable phenotypic effects in their carriers, they were considered genetically inert for a long time. Recent studies on Bs in Apodemus flavicollis revealed their genetic composition, potential origin, and spatial organization in the interphase nucleus. Surprisingly, the genetic content of Bs in this species is preserved in all studied samples, even in geographically distinct populations, indicating its biological importance. Using RT-PCR we studied the transcription activity of three genes (Rraga, Haus6, and Cenpe) previously identified on Bs in A. flavicollis. We analysed mRNA isolated from spleen tissues of 34 animals harboring different numbers of Bs (0–3).The products of transcriptional activity of the analysed sequences differ in individuals with and without Bs. We recorded B-genes and/or genes from the standard genome in the presence of Bs, showing sex-dependent higher levels of transcriptional activity. Furthermore, the transcriptional activity of Cenpe varied with the age of the animals differently in the group with and without Bs. With aging, the amount of product was only found to significantly decrease in B carriers. The potential biological significance of all these differences is discussed in the paper.
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Ding M, Li XY, Zhu ZX, Chen JH, Lu M, Shi Q, Wang Y, Li Z, Zhao X, Wang T, Du WX, Miao C, Yao TZ, Wang MT, Zhang XJ, Wang ZW, Zhou L, Gui JF. Genomic anatomy of male-specific microchromosomes in a gynogenetic fish. PLoS Genet 2021; 17:e1009760. [PMID: 34491994 PMCID: PMC8448357 DOI: 10.1371/journal.pgen.1009760] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/17/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022] Open
Abstract
Unisexual taxa are commonly considered short-lived as the absence of meiotic recombination is supposed to accumulate deleterious mutations and hinder the creation of genetic diversity. However, the gynogenetic gibel carp (Carassius gibelio) with high genetic diversity and wide ecological distribution has outlived its predicted extinction time of a strict unisexual reproduction population. Unlike other unisexual vertebrates, males associated with supernumerary microchromosomes have been observed in gibel carp, which provides a unique system to explore the rationales underlying male occurrence in unisexual lineage and evolution of unisexual reproduction. Here, we identified a massively expanded satellite DNA cluster on microchromosomes of hexaploid gibel carp via comparing with the ancestral tetraploid crucian carp (Carassius auratus). Based on the satellite cluster, we developed a method for single chromosomal fluorescence microdissection and isolated three male-specific microchromosomes in a male metaphase cell. Genomic anatomy revealed that these male-specific microchromosomes contained homologous sequences of autosomes and abundant repetitive elements. Significantly, several potential male-specific genes with transcriptional activity were identified, among which four and five genes displayed male-specific and male-biased expression in gonads, respectively, during the developmental period of sex determination. Therefore, the male-specific microchromosomes resembling common features of sex chromosomes may be the main driving force for male occurrence in gynogenetic gibel carp, which sheds new light on the evolution of unisexual reproduction.
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Affiliation(s)
- Miao Ding
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi-Xuan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Hui Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- ShenZhen People’s Hospital, Shenzhen, China
| | - Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qian Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Xuan Du
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian-Zi Yao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming-Tao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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Abstract
Female meiotic drive is the phenomenon where a selfish genetic element alters chromosome segregation during female meiosis to segregate to the egg and transmit to the next generation more frequently than Mendelian expectation. While several examples of female meiotic drive have been known for many decades, a molecular understanding of the underlying mechanisms has been elusive. Recent advances in this area in several model species prompts a comparative re-examination of these drive systems. In this review, we compare female meiotic drive of several animal and plant species, highlighting pertinent similarities.
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Affiliation(s)
- Frances E. Clark
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Takashi Akera
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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6
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Nascimento-Oliveira JI, Fantinatti BEA, Wolf IR, Cardoso AL, Ramos E, Rieder N, de Oliveira R, Martins C. Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata. BMC Genomics 2021; 22:344. [PMID: 33980143 PMCID: PMC8117508 DOI: 10.1186/s12864-021-07651-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their biology is still enigmatic. Recent advances in omics and big data technologies are revolutionizing the B biology field. These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. Several genes have been detected on the B chromosomes, although the interaction of B sequences and the normal genome remains poorly understood. RESULTS We identified 727 miRNA precursors in the A. latifasciata genome, 66% which were novel predicted sequences that had not been identified before. We were able to report the A. latifasciata-specific miRNAs and common miRNAs identified in other fish species. For the samples carrying the B chromosome (B+), we identified 104 differentially expressed (DE) miRNAs that are down or upregulated compared to samples without B chromosome (B-) (p < 0.05). These miRNAs share common targets in the brain, muscle and gonads. These targets were used to construct a protein-protein-miRNA network showing the high interaction between the targets of differentially expressed miRNAs in the B+ chromosome samples. Among the DE-miRNA targets there are protein-coding genes reported for the B chromosome that are present in the protein-protein-miRNA network. Additionally, Gene Ontology (GO) terms related to nuclear matrix organization and response to stimulus are exclusive to DE miRNA targets of B+ samples. CONCLUSIONS This study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. We observed that the B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes.
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Affiliation(s)
- Jordana Inácio Nascimento-Oliveira
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | | | - Ivan Rodrigo Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Nathalie Rieder
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Rogerio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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7
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Abstract
Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex chromosome in some of these species. We test two hypotheses of how this giant sex chromosome may have evolved. The first hypothesis proposes that it evolved by accumulating repetitive elements as recombination was reduced around a dominant sex determination locus, as suggested by canonical models of sex chromosome evolution. An alternative hypothesis is that the giant sex chromosome originated via the fusion of an autosome with a highly repetitive B chromosome, one of which carried a sex determination locus. We test these hypotheses using comparative analysis of chromosome-scale cichlid and teleost genomes. We find that the giant sex chromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. The WZ sex determination locus encompasses the last ∼105 Mb of the 134-Mb giant chromosome. The last 47 Mb of the giant chromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal that the giant sex chromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long noncoding RNAs. The results favor the B chromosome fusion hypothesis for the origin of the giant chromosome.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Frances E Clark
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Reade B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Qi Zhou
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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8
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Martins C, Jehangir M. A genomic glimpse of B chromosomes in cichlids. Genes Genomics 2021; 43:199-208. [PMID: 33547625 DOI: 10.1007/s13258-021-01049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND B chromosomes (Bs) are extra karyotype elements in addition to A chromosomes and are found in all major eukaryotic taxa. Among hundreds of investigated species, cichlid fishes have emerged as an interesting group of model and have contributed to unravel the complex biology of B chromosome. OBJECTIVE We review the current state of knowledge on B chromosome investigation in cichlid fish and discuss the recent genomic advances over gene and sequences hunting on Bs and their impact on the current concept of B chromosomes. RESULTS The Bs of cichlids have been under the subject of classical cytogenetics and high scale DNA, RNA and epigenetics analysis and a list of B chromosome genes and functional sequences has been generated. B chromosomes of cichlids are restricted to females in some species and are enriched with genes, relics of genes, transposable elements and sequences transcribing for many significant biological functions. Diverse potentially functional sequences have been described in the B chromosome of cichlids and could influence important biological characteristics as well seems to affect transcription and epigenetic modifications of the whole genome. CONCLUSION One of the most enigmatic characteristics of Bs in cichlids is their genic content related to cell cycle and chromosome structure, and their influence over sex rates. The relationship of Bs with cell cycle and sex determination looks like to be connected with the drive of the Bs during cell divisions.
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Affiliation(s)
- Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
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9
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Feller AF, Ogi V, Seehausen O, Meier JI. Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages. HYDROBIOLOGIA 2021; 848:3727-3745. [PMID: 34720170 PMCID: PMC8550731 DOI: 10.1007/s10750-021-04560-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 05/02/2023]
Abstract
UNLABELLED Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10750-021-04560-7.
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Affiliation(s)
- Anna F. Feller
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Vera Ogi
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Joana I. Meier
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
- St John’s College, University of Cambridge, St John’s Street, Cambridge, CB2 1TP UK
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10
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Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia. Genes (Basel) 2020; 11:genes11091017. [PMID: 32872430 PMCID: PMC7563666 DOI: 10.3390/genes11091017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.
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11
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Serrano-Freitas ÉA, Silva DMZA, Ruiz-Ruano FJ, Utsunomia R, Araya-Jaime C, Oliveira C, Camacho JPM, Foresti F. Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes. Mol Genet Genomics 2019; 295:195-207. [PMID: 31624915 DOI: 10.1007/s00438-019-01615-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/01/2019] [Indexed: 12/28/2022]
Abstract
The origin of supernumerary (B) chromosomes is clearly conditioned by their ancestry from the standard (A) chromosomes. Sequence similarity between A and B chromosomes is thus crucial to determine B chromosome origin. For this purpose, we compare here the DNA sequences from A and B chromosomes in the characid fish Characidium gomesi using two main approaches. First, we found 59 satellite DNA (satDNA) families constituting the satellitome of this species and performed FISH analysis for 18 of them. This showed the presence of six satDNAs on the B chromosome: one shared with sex chromosomes and autosomes, two shared with sex chromosomes, one shared with autosomes and two being B-specific. This indicated that B chromosomes most likely arose from the sex chromosomes. Our second approach consisted of the analysis of five repetitive DNA families: 18S and 5S ribosomal DNA (rDNA), the H3 histone gene, U2 snDNA and the most abundant satDNA (CgoSat01-184) on DNA obtained from microdissected B chromosomes and from B-lacking genomes. PCR and sequence analysis of these repetitive sequences was successful for three of them (5S rDNA, H3 histone gene and CgoSat01-184), and sequence comparison revealed that DNA sequences obtained from the B chromosomes displayed higher identity with C. gomesi genomic DNA than with those obtained from other Characidium species. Taken together, our results support the intraspecific origin of B chromosomes in C. gomesi and point to sex chromosomes as B chromosome ancestors, which raises interesting prospects for future joint research on the genetic content of sex and B chromosomes in this species.
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Affiliation(s)
- Érica A Serrano-Freitas
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.,Centro de Ciências Biológicas e da Saúde, Fundação Educacional de Penápolis, Funepe, Penápolis, SP, 16303-180, Brazil
| | - Duílio M Z A Silva
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.
| | - Francisco J Ruiz-Ruano
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Cristian Araya-Jaime
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, 1720256, La Serena, Chile.,Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena, 1720256, La Serena, Chile
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | | | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
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12
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Majtánová Z, Indermaur A, Nyom ARB, Ráb P, Musilova Z. Adaptive Radiation from a Chromosomal Perspective: Evidence of Chromosome Set Stability in Cichlid Fishes (Cichlidae: Teleostei) from the Barombi Mbo Lake, Cameroon. Int J Mol Sci 2019; 20:ijms20204994. [PMID: 31601021 PMCID: PMC6834198 DOI: 10.3390/ijms20204994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely Konia eisentrauti, Konia dikume, Myaka myaka, Pungu maclareni, Sarotherodon steinbachi, Sarotherodon lohbergeri, Sarotherodon linnellii, Sarotherodon caroli, Stomatepia mariae, Stomatepia pindu, and Stomatepia mongo. These species supposedly evolved via sympatric ecological speciation from a common ancestor, which colonized the lake no earlier than one million years ago. Here we present the first comparative cytogenetic analysis of cichlid species from Barombi Mbo Lake using both conventional (Giemsa staining, C-banding, and CMA3/DAPI staining) and molecular (fluorescence in situ hybridization with telomeric, 5S, and 28S rDNA probes) methods. We observed stability on both macro and micro-chromosomal levels. The diploid chromosome number was 2n = 44, and the karyotype was invariably composed of three pairs of meta/submetacentric and 19 pairs of subtelo/acrocentric chromosomes in all analysed species, with the same numbers of rDNA clusters and distribution of heterochromatin. The results suggest the evolutionary stability of chromosomal set; therefore, the large-scale chromosomal rearrangements seem to be unlikely associated with the sympatric speciation in Barombi Mbo.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic.
| | - Adrian Indermaur
- Zoological Institute, University of Basel, 4051 Basel, Switzerland.
| | - Arnold Roger Bitja Nyom
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré P.O Box 454, Cameroon.
- Department of Management of Fisheries and Aquatic Ecosystems, University of Douala, Douala P.O Box 2701, Cameroon.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic.
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University in Prague, 12844 Prague, Czech Republic.
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13
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Wagner Werneck Félix da Costa G, de Bello Cioffi M, Liehr T, Feldberg E, Antonio Carlos Bertollo L, Franco Molina W. Extensive Chromosomal Reorganization in Apistogramma Fishes (Cichlidae, Cichlinae) Fits the Complex Evolutionary Diversification of the Genus. Int J Mol Sci 2019; 20:E4077. [PMID: 31438504 PMCID: PMC6747227 DOI: 10.3390/ijms20174077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Neotropical cichlid fishes are one of the most diversified and evolutionarily successful species assemblages. Extremely similar forms and intraspecific polychromatism present challenges for the taxonomy of some of these groups. Several species complexes have a largely unknown origin and unresolved evolutionary processes. Dwarf cichlids of the genus Apistogramma, comprising more than a hundred species, exhibit intricate taxonomic and biogeographic patterns, with both allopatric and sympatric distributions. However, karyotype evolution and the role of chromosomal changes in Apistogramma are still unknown. In the present study, nine South American Apistogramma species were analyzed using conventional cytogenetic methods and the mapping of repetitive DNA sequences [18S rDNA, 5S rDNA, and (TTAGGG)n] by fluorescence in situ hybridization (FISH). Our results showed that Apistogramma has unique cytogenetic characteristics in relation to closely related groups, such as a reduced 2n and a large number of bi-armed chromosomes. Interspecific patterns revealed a scenario of remarkable karyotypic changes, including a reduction of 2n, the occurrence of B-chromosomes and evolutionary dynamic of rDNA tandem repeats. In addition to the well-known pre-zygotic reproductive isolation, the karyotype reorganization in the genus suggests that chromosomal changes could act as postzygotic barriers in areas where Apistogramma congeners overlap.
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Affiliation(s)
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, Friedrich Schiller University, Am Klinikum 1, 07747 Jena, Germany.
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Laboratório de Genética Animal, Av. André Araújo, 2936, Manaus 69077-000, AM, Brazil
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, Km. 235, C.P. 676, São Carlos 13565-905, SP, Brazil
| | - Wagner Franco Molina
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal 59078-970, RN, Brazil
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14
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Jehangir M, Ahmad SF, Cardoso AL, Ramos E, Valente GT, Martins C. De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes. Chromosoma 2019; 128:81-96. [PMID: 31115663 DOI: 10.1007/s00412-019-00707-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish Astatotilapia latifasciata, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B-), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes. The draft assemblies comprised 771 Mb for the B- genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B- assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.
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Affiliation(s)
- Maryam Jehangir
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Syed F Ahmad
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Guilherme T Valente
- Bioprocess and Biotechnology Department, Agronomical Science Faculty, Sao Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil.
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15
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Houben A, Jones N, Martins C, Trifonov V. Evolution, Composition and Regulation of Supernumerary B Chromosomes. Genes (Basel) 2019; 10:E161. [PMID: 30791610 PMCID: PMC6409906 DOI: 10.3390/genes10020161] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/23/2022] Open
Abstract
Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi [...].
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Affiliation(s)
- Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
| | - Neil Jones
- Aberystwyth University, Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Penglais Campus, Aberystwyth SY23 3DA, UK.
| | - Cesar Martins
- Institute of Bioscience at Botucatu, São Paulo State University-UNESP, Botucatu, SP 18618, Brazil.
| | - Vladimir Trifonov
- Laboratory of Comparative Genomics, Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
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16
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Ahmad SF, Martins C. The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses. Cells 2019; 8:E156. [PMID: 30781835 PMCID: PMC6406668 DOI: 10.3390/cells8020156] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/10/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
Supernumerary B chromosomes (Bs) are extra karyotype units in addition to A chromosomes, and are found in some fungi and thousands of animals and plant species. Bs are uniquely characterized due to their non-Mendelian inheritance, and represent one of the best examples of genomic conflict. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. A classical concept based on cytogenetics and genetics is that Bs are selfish and abundant with DNA repeats and transposons, and in most cases, they do not carry any function. However, recently, the modern quantum development of high scale multi-omics techniques has shifted B research towards a new-born field that we call "B-omics". We review the recent literature and add novel perspectives to the B research, discussing the role of new technologies to understand the mechanistic perspectives of the molecular evolution and function of Bs. The modern view states that B chromosomes are enriched with genes for many significant biological functions, including but not limited to the interesting set of genes related to cell cycle and chromosome structure. Furthermore, the presence of B chromosomes could favor genomic rearrangements and influence the nuclear environment affecting the function of other chromatin regions. We hypothesize that B chromosomes might play a key function in driving their transmission and maintenance inside the cell, as well as offer an extra genomic compartment for evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Department of Morphology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), CEP 18618689, Botucatu, SP, Brazil.
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), CEP 18618689, Botucatu, SP, Brazil.
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